gram stain

METPO:1000697 · CLASS · REVIEWED

A phenotype where microorganisms are grouped based on their ability to retain crystal violet dye in the Gram staining procedure.

Gram stain cell-envelope retention mechanism

Evidence-backed causal sketch linking Gram stain phenotype to crystal violet-iodine complex formation, peptidoglycan architecture, outer membrane loss during decolorization, and counterstaining.

Edge evidence

crystal violet reacts with iodine mordant
Crystal violet and iodine form a dye complex during the Gram stain.
- DOI:10.1128/jb.156.2.837-845.1983 produce a chemical precipitate Supports chemical formation of the crystal violet-iodine precipitate.
crystal violet-iodine complex is retained by peptidoglycan cell wall
Cell-wall architecture determines whether the dye complex remains after decolorization.
- DOI:10.3109/10520299609117151 cell wall ... responsible for retention Review supports the Gram-positive cell wall as responsible for retaining the dye-iodine complex.
alcohol decolorization removes outer membrane
Decolorization disrupts the Gram-negative outer membrane and helps remove dye complex.
- DOI:10.1128/jb.156.2.837-845.1983 alcohol-acetone decolorization Supports decolorization as a chemical step differentiating Gram reactions.
outer membrane regulates gram stain RO:0002211
The Gram-negative outer membrane contributes to dye loss and counterstain appearance.
- DOI:10.1038/s41579-019-0201-x defining feature of the Gram-negative cell envelope Supports the outer membrane as a defining Gram-negative envelope feature.
peptidoglycan cell wall causes gram stain biolink:causes
Peptidoglycan thickness and envelope architecture determine Gram stain outcome.
- DOI:10.3109/10520299609117151 mechanism of the Gram stain Supports cell-wall mediated Gram reaction.

Provenance

Source: METPO (2025-11-25)
Author: Luke Wang
Definition source: DOI:10.3109/10520299609117151

Parent traits (1)

phenotype METPO:1000059

Children (3)

Synonyms (2)

Morphology.cell morphology.gram stain RELATED_SYNONYM · metpo.owl
gram_stain RELATED_SYNONYM · metpo.owl

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

METPO:1000697 [-2.552, -2.118, -3.376, -0.738, …]

512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

Nearest neighbors in embedding space

Top-8 cosine-similar METPO traits from the 2026-04-25 deepwalk (512-D).

morphology gram variable 0.977
upper phenotype 0.763
environment ionizing radiation tolerant 0.763
physiology persister cell formation 0.763
morphology sulfur globule 0.763
morphology S-layer 0.763
morphology prosthecate 0.763
morphology polyphosphate granule 0.763

Curation history

2026-05-05T01:35:46.901879+00:00 · SEEDED_FROM_METPO · seed_from_metpo
imported from data/raw/metpo.owl (CLASS)
2026-05-11T00:00:00-07:00 · CURATED_WITH_LITERATURE · codex
Reviewed Gram stain trait and added DOI-backed causal graph for crystal violet-iodine complex retention, peptidoglycan cell wall architecture, outer membrane influence, and alcohol decolorization.
2026-05-24T04:38:00Z · GROUND_CAUSAL_NODES · claude
Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0019867×1).
2026-05-26T05:00:48Z · RENAME_PREDICATE_LABELS · claude
Renamed 2 causal-edge predicate label(s) to align with existing groundings: influences → regulates ×1; determines → causes ×1.
2026-05-26T05:00:50Z · GROUND_CAUSAL_PREDICATES · claude
Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211×1, biolink:causes×1).
2026-06-14T05:51:46Z · GROUND_CAUSAL_NODES · claude
Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:41688×1).